tests/README.md

In facilebio/FacileData: A fluent API for accessing multi-assay high-throughput genomics data

Tests and Coverage

04 June, 2018 08:06:13

• Coverage
• Unit Tests

This output is created by covrpage.

Coverage

Coverage summary is created using the covr package.

| Object | Coverage (%) | |:------------------------------------------------------------|:------------:| | FacileData | 41.64 | | R/build-db.R | 0.00 | | R/features.R | 0.00 | | R/NSE-filter-features.R | 0.00 | | R/NSE-filter-samples.R | 0.00 | | R/sql.R | 0.00 | | R/construction.R | 4.44 | | R/as.FacileDataSet.R | 5.32 | | R/samples.R | 27.47 | | R/utilities.R | 44.44 | | R/FacileDataSet.R | 50.46 | | R/db-and-table-functions.R | 56.91 | | R/as.BiocAssayContainers.R | 57.55 | | R/entity-attribute-value.R | 60.17 | | R/validation.R | 60.38 | | R/assay-data.R | 65.30 | | R/sample-covariates.R | 75.83 | | R/test-helpers.R | 92.86 | | R/sample-info.R | 93.33 |

Unit Tests

Unit Test summary is created using the testthat package.

| file | n| time| error| failed| skipped| warning| |:------------------------------------------------------------------------|----:|------:|------:|-------:|--------:|--------:| | test-as.FacileDataSet.R | 1| 0.138| 0| 0| 0| 0| | test-assay-data.R | 4| 1.872| 0| 0| 0| 0| | test-bioc-assay-containers.R | 14| 1.151| 0| 0| 0| 0| | test-entity-attribute-value.R | 46| 0.165| 0| 0| 0| 0| | test-FacileDataSet.R | 3| 0.023| 0| 0| 0| 0| | test-sample-covariates.R | 24| 1.035| 0| 0| 0| 0| | test-samples.R | 1| 0.032| 0| 0| 0| 0| | test-utilities.R | 2| 0.014| 0| 0| 0| 0|

| file | test | context | status | n| time| |:------------------------------------------------------------------------|:--------------------------------------------------------------------|:-------------------------------------------------|:-------|----:|------:| | test-as.FacileDataSet.R | We can get pdata metadata | as.FacileDataSet | PASS | 1| 0.138| | test-assay-data.R | fetch_assay_data limits samples correctly | Fetching assay level data | PASS | 2| 0.753| | test-assay-data.R | spreading data works with_assay_data | Fetching assay level data | PASS | 1| 0.518| | test-assay-data.R | fetch_assay_data(..., aggregate.by='ewm') provides scores | Fetching assay level data | PASS | 1| 0.601| | test-bioc-assay-containers.R | fetch_assay_data results converted to DGEList | Testing conversion to Bioc Expression Containers | PASS | 14| 1.151| | test-entity-attribute-value.R | pData -> meta.yaml covariate encoding works (simple & compound) | Entity-Attribute-Value conversions | PASS | 44| 0.162| | test-entity-attribute-value.R | basic encoding and decoding of EAV columns works | Entity-Attribute-Value conversions | PASS | 2| 0.003| | test-FacileDataSet.R | Fetching various database tables from FacileDataSet | Basic FacileDataSet functions | PASS | 3| 0.023| | test-sample-covariates.R | fetch_sample_covariates retrieves all covariates if not specified | Sample Covariates | PASS | 1| 0.084| | test-sample-covariates.R | fetch_sample_covariates::samples arg limits samples correctly | Sample Covariates | PASS | 1| 0.035| | test-sample-covariates.R | cast_covariate converts simple variables to correct type | Sample Covariates | PASS | 6| 0.085| | test-sample-covariates.R | cast_covariate converts right_censored data correctly | Sample Covariates | PASS | 8| 0.061| | test-sample-covariates.R | spread_covariates casts simple covariates to correct class | Sample Covariates | PASS | 4| 0.047| | test-sample-covariates.R | spread_covariates works with both simple and complex types | Sample Covariates | PASS | 2| 0.111| | test-sample-covariates.R | with_sample_covariates returns long input with wide covariates | Sample Covariates | PASS | 1| 0.517| | test-sample-covariates.R | successive with_sample_covariate calls build correct frame | Sample Covariates | PASS | 1| 0.095| | test-samples.R | fetch samples returns valid sample descriptor absent assay spec | Retrieving arbitrary samples | PASS | 1| 0.032| | test-utilities.R | We can bind_rows data.frames with Surv columns | | PASS | 2| 0.014|

facilebio/FacileData documentation built on Feb. 23, 2024, 9:14 a.m.